The Environment Department says soil being used to build water regulators on the Goolwa Channel, Currency Creek and the Finniss River is from expansion of the Hindmarsh Island marina.

Department chief executive Allan Holmes says it is costing about $20 million to build the three regulators in efforts to reduce a spread of acid sulfate soils in the Murray's lower lakes due to drought and create freshwater refuges.

Mr Holmes says it was not his role to decide where the hundreds of thousands of tonnes of soil came from.

"We contracted a company to construct the wall, it was up to them to source the material," he said.

"As it happens they are sourcing that material from the cheapest place, as you would expect.

"And the cheapest place for them source it is from the construction of some sort of channel as part of the marina. That's not our business, that's what happened."

Democrats MP David Winderlich is calling for more information about the source and cost of soil being used to build the regulators, saying there is talk of a sweetheart deal.

"The easiest way to put that to rest is for the Department of Environment simply to release its figures so everyone can see that this dirt was bought at the least cost price and not to prop up any particular interests," he said.

Hindmarsh Island marina owner Andrew Chapman has not been available for comment.

'Necessary?'

An Aboriginal elder from the lower lakes region says the Government should re-evaluate its decision to build the three regulators.

Tom Trevorrow says winter rains have boosted water levels, which is bringing bird life back to the lower Murray region.

"The waters are looking good, so we are very concerned at the moment that is this really necessary, should the government be stopping, having a look at the situation, re-evaluating it and putting together and really think before this goes any further?" he said.

Ongoing drought conditions have exposed 20,000 hectares of river and lake beds and the soil has become toxic.

The SA Government says the flow regulators will help keep the soil wet to fight acidification.